Hello,
I have an anndata object from a sample that I am processing through scanpy. I have reached the point where I did the leiden clustering. I would like to export to a csv file all the genes expressed in each cluster and the counts for each gene.
df_gene_expression = pd.DataFrame(adata.X, index=adata.obs.index, columns=adata.var.index)
df_gene_expression[‘cluster’] = adata.obs[‘leiden_0.4’]
The above seems to work but I also want to do this for the adata.raw data.
I first did the below and then run the command to create the dataframe again.
ad5 = adata.raw.to_adata()
I get this message:
ValueError: Shape of passed values is (11647, 1), indices imply (11647, 18845)
I looked at the ad5.X and it looks like this:
<11647x18845 sparse matrix of type ‘<class ‘numpy.float32’>’
with 16326262 stored elements in Compressed Sparse Row format>
How can I use it properly to export the list?
Thank you